The aphylo
class tree holds both the tree structure represented as a
partially ordered phylogenetic tree, and node annotations. While annotations
are included for both leafs and inner nodes, the algorithms included in this
package only uses the leaf annotations.
new_aphylo(tree, tip.annotation, ...)
# S3 method for phylo
new_aphylo(
tree,
tip.annotation,
node.annotation = NULL,
tip.type = NULL,
node.type = NULL,
...
)
A list of class aphylo
with the following elements:
An object of class phylo.
An integer matrix. Tip (leaf) nodes annotations.
An integer matrix (optional). Internal nodes annotations.
A list. List of offspring of each node.
Integer vector. The pruning sequence (postorder).
Integer vector. The reduced version of pseq
.
Integer. Number of tips with annotations.
Binary of length Ntip()
. 0 means duplication and 1 speciation.
Binary of length Nnode()
. 0 means duplication and 1 speciation.
Other Data management functions:
aphylo_from_data_frame()
Other aphylo methods:
aphylo-methods